Structure of PDB 3o0o Chain A Binding Site BS04

Receptor Information
>3o0o Chain A (length=612) Species: 2336 (Thermotoga maritima) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKLSDLISRWIDVEPSKNAQIILRDRYFMKDLDGNYLETKWEDVARRVAR
VVATAELLNPSKLDRIKEWEDIFFRVLKARLFIPNSPTLFNAGLGVKHDL
LWKPIDQMTLEDYEEIYRSRNHLHMLSACFVVPVGDSIEEIFEAVKEYAL
ITKVGGGVGSNFSELRPKGSFVAGTHGKASGPVSFMHVFNSAISVVKQGS
RRGALMGILNINHPDIEEFIDAKKVLNFFNLSVGFPMDKKEILKLYEEDG
ELELSHPRSTIRKKVKIRELFRKIATNAWKSGDPGLAFLGEMNKYYPLYP
HRKINSTNPCGEIGLSDYEACNLGSIDVAKFYNNGFVDLEALQELVQIAV
RFLDNVIDVNVFPIDKITKAVKESRRLGLGIMGFADLLYKLEIPYNSQEA
RDFAANLMAFIALHAHRTSYELGKEKGNFPLLEISRYRTEDNFVPFAMGM
SNYDDEIREVMKMTKEFRRNVALLTIAPTGSISNIADTSSGLEPNFLLAY
TRFPLLYVNQVLREKLNPEILKRIEKELIEKGSLKDIPDVPEKIKKVFVV
ALDIDPMDHLLMQDAFQRYVDNNISKTINMPQSATVDDVLNVYLEALRTN
VRGITVYRDGSL
Ligand information
Ligand IDTTP
InChIInChI=1S/C10H17N2O14P3/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(24-8)4-23-28(19,20)26-29(21,22)25-27(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,19,20)(H,21,22)(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
InChIKeyNHVNXKFIZYSCEB-XLPZGREQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O
CACTVS 3.341CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C(=C1)C)CC2O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
CACTVS 3.341CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
FormulaC10 H17 N2 O14 P3
NameTHYMIDINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL363559
DrugBankDB02452
ZINCZINC000008215959
PDB chain3o0o Chain B Residue 1001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3o0o Structural Basis for Adenosylcobalamin Activation in AdoCbl-Dependent Ribonucleotide Reductases.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		K158 K202
Binding residue
(residue number reindexed from 1)		K153 K197
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) C134 N320 C322 E324 C333 T626 V627
Catalytic site (residue number reindexed from 1) C129 N308 C310 E312 C321 T605 V606
Enzyme Commision number 1.17.4.1: ribonucleoside-diphosphate reductase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0004748 ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor
GO:0005524 ATP binding
GO:0031419 cobalamin binding
Biological Process
GO:0009263 deoxyribonucleotide biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3o0o, PDBe:3o0o, PDBj:3o0o
PDBsum3o0o
PubMed20672854
UniProtO33839

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